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Applications of Python in Neuroimaging
Alexander Holmes edited this page Jul 5, 2023
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9 revisions
- 0.0 Home
- 0.1 Neuroscience fundamentals
- 0.2 Reproducible Science
- 0.3 MRI Physics, BIDS, DICOM, and data formats
- 0.4 Introduction to Diffusion MRI
- 0.5 Introduction to Functional MRI
- 0.6 Measuring functional and effective connectivity
- 0.7 Connectomics, graph theory, and complexity
- 0.8 Statistical and Mathematical Tidbits
- 0.9 Introduction to Psychopathology
- 0.10 Introduction to Genetics and Bioinformatics
- 0.11 Introduction to Programming
- 1.0 Working on the Cluster
- 2.0 Programming Languages
- 2.1 Python
- 2.2 MATLAB
- 2.3 R and RStudio
- 2.4 Programming Intro Exercises
- 2.5 git and GitHub
- 2.6 SLURM and Job Submission
- 3.0 Neuroimaging Tools and Packages
- 3.1 BIDS
- 3.2 FreeSurfer
- 3.2.1 Qdec
- 3.3 FSL
- 3.3.1 ICA-FIX
- 3.4 Connectome Workbench/wb_command
- 3.5 fMRIPrep
- 3.6 QSIPrep
- 3.7 HCP Pipeline
- 3.8 tedana
- 4.0 Quality control
- 4.1 MRIQC
- 4.2 Common Artefacts
- 4.3 T1w
- 4.4 rs-fMRI
- 5.0 Specialist Tools
- 6.0 Putting it all together
- 7.0 Data management